Article
Chemistry, Analytical
Tong Li, Mengxu Sun, Suping Xia, Ting Huang, Rong-Tian Li, Chunrong Li, Zong Dai, Jin-Xiang Chen, Jun Chen, Nuan Jia
Summary: Here, we developed a binary system based on DNA tetrahedron and fluorogenic RNA aptamers for highly specific and label-free mRNA imaging in living cells. This system achieved high specificity label-free detection of nucleic acids with a detection limit of 1.34 nM. The method has potential applications in early disease diagnosis and new drug development.
Article
Biochemical Research Methods
Simon J. Moore, Hung-En Lai, Soo-Mei Chee, Ming Toh, Seth Coode, Kameshwari Chengan, Patrick Capel, Christophe Corre, Emmanuel L. C. de los Santos, Paul S. Freemont
Summary: TX-TL systems show promise in studying natural product biosynthetic pathways with reduced experimental time and controlled conditions. Developing specialized cell-free systems is crucial, and the updated Streptomyces TX-TL protocol improves protein yield, demonstrating combined transcription, translation, and biosynthesis of Streptomyces metabolic pathways in a single reaction pot.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Qiuyu Lu, Yaxin Hu, Cheuk Yin Li, Yi Kuang
Summary: This study introduces a readout control module that reduces protein leakage in synthetic mRNA switches, thereby decreasing signal noise and increasing input sensitivity and output range. These switches are applicable to different types of input molecules and output proteins, offering potential for accurate cell manipulation in biomedical applications.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biology
Conary Meyer, Yusuke Nakamura, Blake J. Rasor, Ashty S. Karim, Michael C. Jewett, Cheemeng Tan
Summary: Cell-free synthetic biology is a mature field with key features such as bypassing evolution mechanisms, circumventing molecular transport limitations across cell walls, and providing high yield and tolerance. Analysis shows an increase in patent filings and publications, changes in innovation landscape, and a growing prevalence of biotechnology companies using cell-free systems.
Article
Biotechnology & Applied Microbiology
Xinlei Wei, Qiangzi Li, Congcong Hu, Chun You
Summary: A novel approach for stoichiometric synthesis of mannitol through an in vitro synthetic enzymatic biosystem using low-cost starch as substrate is proposed in this study. The overall reaction pathway is divided into three modules which could be executed sequentially in one pot. High product yields of around 95-98% were achieved under optimized conditions.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Biochemical Research Methods
Jiang He, Lior Nissim, Ava P. Soleimany, Adina Binder-Nissim, Heather E. Fleming, Timothy K. Lu, Sangeeta N. Bhatia
Summary: The integration of nanotechnology and synthetic biology has led to the development of a gene circuit that can amplify biosensor responses to cancer states.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Inseong Choi, Guk-Young Ahn, Eun Seo Kim, Se Hee Hwang, Hyo-Jung Park, Subin Yoon, Jisun Lee, Youngran Cho, Jae-Hwan Nam, Sung-Wook Choi
Summary: A new microfluidic bioreactor was developed with fibrous micromixers for ingredient mixing and a long macrochannel for in vitro transcription reaction, enabling continuous production of mRNA. The diameter of the fibrous microchannels in the micromixers was controlled by using an electrospun microfibrous disc with different microfiber diameters. The micromixer with larger diameter fibrous microchannels showed superior mixing performance. The continuous reaction in the microfluidic bioreactor with efficient mixing performance can serve as a powerful platform for various microfluidic reactions.
Article
Chemistry, Inorganic & Nuclear
Hao Yuan, Tao Wang, Tong Zhu, Zhihui Feng, Fei Wang, Yupeng Tian, Liulin Xiong, Xiaohe Tian
Summary: Interactions between lipid droplets (LDs) and mitochondria are crucial for beta-oxidation and fatty acid (FA) storage. Studying these interactions using fluorescent dyes often faces limitations such as low signal-to-noise ratios and overlapping spectra. To overcome this issue, a series of rare earth complexes named Eu(TTA)(3)-L1-3 were developed. In particular, Eu(TTA)(3)-L3, which changes from a 'turn-off' to a 'turn-on' fluorescence state upon interacting with RNA, was successfully used to monitor changes in LDs and mitochondria under two-photon conditions during oleic acid treatment and starvation-induced autophagy. This research provides an effective tool for comprehensive study of LDs and mitochondria interaction and expands the possibilities for designing dual-targeting single fluorescent probes.
INORGANIC CHEMISTRY FRONTIERS
(2023)
Review
Plant Sciences
Constantine Garagounis, Nikolaos Delkis, Kalliope K. Papadopoulou
Summary: Plants are a rich source of biologically active compounds, but the functions of these compounds are often unclear due to dynamic production and accumulation. Constructing biosensors using synthetic biology strategies to detect specialized metabolites can help determine their precise localization and develop system-level models to understand how their biosynthesis interacts with plant growth and development.
Review
Biotechnology & Applied Microbiology
Jing Sheng, Yan Pi, Shuang Zhao, Binpan Wang, Ming Chen, Kai Chang
Summary: DNA nanoflowers (DNFs) are topological flower-like nanostructures made of long-strand DNA and inorganic metal-ion frameworks. They are programmable, biocompatible, and can assemble to specific sizes for detecting biomolecules. This review covers the current state of DNF-based biosensing strategies for in vivo and in vitro detection, discusses their classification, and explores future applications. DNFs can accelerate biosensing engineering by amplifying signals. The key challenges and prospects of DNF-based biosensing technologies are also discussed.
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Kaixin Tan, Yaxin Hu, Zhenghua Liang, Cheuk Yin Li, Wai Laam Yau, Yi Kuang
Summary: Synthetic mRNA circuits control output protein expression by detecting specific input molecules in cells. Existing circuits either enhance or repress protein production upon input binding, but this binary mechanism limits precise control. In this study, bidirectional mRNA circuits were designed to independently control enhancer and repressor modules using different input molecules, resulting in fine-tuning of protein expression. This research expands the capabilities of synthetic mRNA circuits for precise cell manipulation and provides cell-based solutions to biomedical problems.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biophysics
Tomoyuki Taguchi, Machi Ishikawa, Momoko Ichikawa, Takashi Tadenuma, Yuko Hirakawa, Tomoko Yoshino, Yoshiaki Maeda, Hiyori Takeuchi, Daisuke Nojima, Takeo Tanaami, Tadashi Matsunaga, Tsuyoshi Tanaka
Summary: In this study, a novel DNA microarray system was developed that eliminates the need for labeling, amplification, or washing of target nucleic acid fragments. By using specially designed DNA probes, the system allows for quick and specific detection of DNA and RNA within a short period of time.
BIOSENSORS & BIOELECTRONICS
(2021)
Article
Chemistry, Analytical
Francisco Fueyo-Gonzalez, Rosario Herranz, Simona Plesselova, Maria D. Giron, Rafael Salto, Jose Manuel Paredes, Angel Orte, May C. Morris, Juan A. Gonzalez-Vera
Summary: CDK5 kinase is activated through interactions with different partners, playing a key role in neuronal functions and contributing to neurodegenerative diseases and human cancers. The design of fluorescently labeled peptides allowed for the detection of CDK5 partners, demonstrating the potential of the biosensor to report on the relative abundance of p25.
SENSORS AND ACTUATORS B-CHEMICAL
(2021)
Article
Plant Sciences
Arjun Khakhar, Daniel F. Voytas
Summary: The tools of synthetic biology offer great potential to uncover fundamental mechanisms in plant development and metabolism, but typically require transgenesis. Delivery of foreign genetic material to plants using systemically mobile RNA virus vectors can minimize transgenesis, revolutionizing plant synthetic biology by reducing costs, accelerating experimental timescales, and making genetic manipulation easier.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Endocrinology & Metabolism
Rui Sheng, Yuan Wang, Yunshu Wu, Jun Wang, Shiwen Zhang, Qiwen Li, Danting Zhang, Xingying Qi, Qingyue Xiao, Shuang Jiang, Quan Yuan
Summary: This study reveals the crucial role of m(6)A methyltransferase METTL3 in tooth root development by influencing NFIC translation efficiency, shedding light on a novel epigenetic mechanism in tooth root formation.
JOURNAL OF BONE AND MINERAL RESEARCH
(2021)
Article
Multidisciplinary Sciences
Zoe Swank, Gregoire Michielin, Hon Ming Yip, Patrick Cohen, Diego O. Andrey, Nicolas Vuilleumier, Laurent Kaiser, Isabella Eckerle, Benjamin Meyer, Sebastian J. Maerkl
Summary: A novel microfluidic nanoimmunoassay technology has been developed for high-throughput detection of anti-SARS-CoV-2 IgG antibodies in human blood samples, showing high specificity and sensitivity. Using two commercial devices and a blood glucose test strip, a low-cost and ultralow-volume whole blood sampling method without the need for venipuncture has been successfully achieved. This technology is expected to be applicable to current and future SARS-CoV-2 related serological studies.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Multidisciplinary
Simone Giaveri, Adeline Marie Schmitt, Laura Roset Julia, Vincenzo Scamarcio, Anna Murello, Shiyu Cheng, Laure Menin, Daniel Ortiz, Luc Patiny, Sreenath Bolisetty, Raffaele Mezzenga, Sebastian Josef Maerkl, Francesco Stellacci
Summary: Plastic pollution poses a significant challenge to humanity, while proteins, as sustainable natural polymers, can be recycled and used to produce new proteins like GFP.
ADVANCED MATERIALS
(2021)
Article
Multidisciplinary Sciences
Laura Grasemann, Barbora Lavickova, M. Carolina Elizondo-Cantu, Sebastian J. Maerkl
Summary: The PURE system is a promising chassis for cell-free synthetic biology, but commercially available systems are expensive while homemade methods are time-consuming and laborious. Streamlining protein purification through coculturing and co-purification can minimize time and labor requirements.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Chemistry, Multidisciplinary
Fabien Jammes, Julien Schmidt, George Coukos, Sebastian J. Maerkl
Summary: We have developed an integrated microfluidic cellular processing unit that can autonomously isolate and analyze the cell-surface dissociation rates, and recover selected cells. By performing high-throughput single-cell experiments, we have characterized the pMHC-TCR interactions on live CD8+ T cells.
Letter
Infectious Diseases
Elsa Lorthe, Mathilde Bellon, Julie Berthelot, Gregoire Michielin, Arnaud G. L'Huillier, Klara M. Posfay-Barbe, Andrew S. Azman, Idris Guessous, Sebastian J. Maerkl, Isabella Eckerle, Silvia Stringhini
LANCET INFECTIOUS DISEASES
(2022)
Review
Biotechnology & Applied Microbiology
Ragunathan Bava Ganesh, Sebastian J. Maerkl
Summary: Cell-free biology is increasingly used for engineering biological systems and bypassing the limitations associated with cells. This review focuses on the role of aminoacyl tRNA synthetases and tRNA in translation and protein synthesis, summarizes the progress in cell-free engineering of tRNAs and AARSs, and discusses the prospects and challenges in this field.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Elsa Lorthe, Mathilde Bellon, Gregoire Michielin, Julie Berthelot, Maria-Eugenia Zaballa, Francesco Pennacchio, Meriem Bekliz, Florian Laubscher, Fatemeh Arefi, Javier Perez-Saez, Andrew S. Azman, Arnaud G. L'Huillier, Klara M. Posfay-Barbe, Laurent Kaiser, Idris Guessous, Sebastian J. Maerkl, Isabella Eckerle, Silvia Stringhini
Summary: This study reports the findings of a prospective epidemiological, virological, and serological investigation of a SARS-CoV-2 outbreak in a primary school. The results demonstrate child-to-child and child-to-adult transmission of SARS-CoV-2, as well as its introduction into households. Effective measures to limit transmission in schools have the potential to reduce community circulation.
Article
Multidisciplinary Sciences
Amir Shahein, Maria Lopez-Malo, Ivan Istomin, Evan J. Olson, Shiyu Cheng, Sebastian J. Maerkl
Summary: This research provides a detailed characterization of low-affinity binding site clusters, showing that transcription factors can bind concurrently to overlapping sites, challenging the exclusivity of binding. Furthermore, even small clusters with low-affinity binding sites can achieve high occupancies at physiologically-relevant transcription factor concentrations. In vivo experiments demonstrate that low-affinity binding site clusters can generate transcriptional output comparable to consensus sites.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Hon Ming Yip, Shiyu Cheng, Evan J. Olson, Michael Crone, Sebastian J. Maerkl
Summary: Cells have the ability to adapt to changing environmental conditions through regulatory networks. The Pho regulon in Saccharomyces cerevisiae is one such system that activates in low phosphate concentration to scavenge phosphate. However, the precise mechanism of this regulon was unclear until a systems analysis on single cells revealed an intermediate nuclear localization state of the transcriptional master regulator Pho4p. This finding explains the observed programmatic states of the regulon and improves our understanding of gene regulatory networks.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Gregoire Michielin, Sebastian J. Maerkl
Summary: This study presents a method for directly encapsulating active biomolecules in semi-permeable microcapsules, achieved by using microcapsules made from poly(ethylene glycol) diacrylate. The method can be used for protecting biological active substances, encapsulating enzymes, and implementing compartmentalized DNA strand displacement reactions.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Barbora Lavickova, Laura Grasemann, Sebastian J. Maerkl
Summary: The protein synthesis capacity of the PURE cell-free transcription-translation system can be significantly enhanced by using continuous dialysis via semipermeable membranes and chemostat operation, providing a promising technological basis for complex cell-free synthetic biology applications that require improved protein synthesis capacity.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Gregoire Michielin, Fatemeh Arefi, Olha Puhach, Mathilde Bellon, Pascale Sattonnet-Roche, Arnaud G. L'Huillier, Isabella Eckerle, Benjamin Meyer, Sebastian J. Maerkl
Summary: This study evaluates the diagnostic performance of dried blood microsampling combined with a high-throughput microfluidic nano-immunoassay (NIA) for identifying anti-SARS-CoV-2 Spike IgG seropositivity. The results show that the combination of microsampling and NIA achieves a clinical sensitivity of 98.33% and specificity of 97.62% in individuals 11 months post infection, demonstrating the high performance of NIA.
Article
Biochemical Research Methods
Julia Tischler, Zoe Swank, Hao-An Hsiung, Stefano Vianello, Matthias P. Lutolf, Sebastian J. Maerkl
Summary: This study presents a low-cost system for controlling complex mammalian cell culture by combining conventional multi-well tissue culture plates with simple microfluidic control and system automation. The system allows for the generation of complex concentration profiles and has been applied to dynamic stimulation of stem-cell-based in vitro models for mammalian development. The results show that this system is a versatile and scalable tool that can be adapted to specific research questions and experimental demands.
CELL REPORTS METHODS
(2022)
Correction
Biochemical Research Methods
Julia Tischler, Zoe Swank, Hao-An Hsiung, Stefano Vianello, Matthias P. Lutolf, Sebastian J. Maerkl
CELL REPORTS METHODS
(2022)
Article
Chemistry, Multidisciplinary
Christy J. Cho, Henrike Niederholtmeyer, Hyeonglim Seo, Ahanjit Bhattacharya, Neal K. Devaraj
Summary: This study systematically characterizes the interaction of DNA with lipid sponge droplets, demonstrating a strong size dependence for DNA functionalization. Shorter DNA molecules efficiently partition into the lipid sponge phase and can direct DNA-templated reactions to droplets. This system opens new opportunities for DNA-encoded functions in lipid sponge droplets.